Comments (9)
MikkelSchubert
commented on August 23, 2024
Hi,
That sounds odd.
Can you try to copy/paste the exact command you used to run AdapterRemoval?
While I would not expect the output to be an empty file, running
AdapterRemoval on a file without adapter sequences will still cause
changes. The algorithm used by AdapterRemoval does not have perfect
specificity, so false positives are to be expected. That said, I am only
seeing a few potentially false positives when I run AdapterRemoval on those
files.
Best regards,
Mikkel
…On Tue, Dec 18, 2018 at 6:22 PM Billy Taj ***@***.***> wrote:
Hi,
I'm trying to use your tool on a dataset that has no adapters.
However, the output of the program is a completely blank Fastq. Shouldn't
it leave my file alone, if there are no adapters?
The data I used is from here: http://huttenhower.sph.harvard.edu/humann2
Their synthetic human gut rna sample.
I am using factory default settings, and fastqc tells me this sample has
no adapters.
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billytaj
commented on August 23, 2024
>&2 echo Removing adapters | /pipeline_tools/adapterremoval/AdapterRemoval --file1 /scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/0_sorted_raw_input/pair_1_sorted.fastq --file2 /scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/0_sorted_raw_input/pair_2_sorted.fastq --qualitybase 33 --threads 80 --minlength 30 --basename /scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/1_adapter_removal_AdapterRemoval --trimqualities --output1 /scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/1_adapter_removal/pair_1_adptr_rem.fastq --output2 /scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/1_adapter_removal/pair_2_adptr_rem.fastq --singleton /scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/1_adapter_removal/singletons_adptr_rem.fastq
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MikkelSchubert
commented on August 23, 2024
That looks fine, though I don't think you'll gain much from using 80
threads.
You said that the output "is a completely blank Fastq".
Does that apply to all of the resulting FASTQ files? That is to say, are
pair_1_adptr_rem.fastq, pair_2_adptr_rem.fastq, and
singletons_adptr_rem.fastq all empty?
…On Tue, Dec 18, 2018 at 7:29 PM Billy Taj ***@***.***> wrote:
&2 echo Removing adapters | /pipeline_tools/adapterremoval/AdapterRemoval
--file1
/scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/0_sorted_raw_input/pair_1_sorted.fastq
--file2
/scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/0_sorted_raw_input/pair_2_sorted.fastq
--qualitybase 33 --threads 80 --minlength 30 --basename
/scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/1_adapter_removal_AdapterRemoval
--trimqualities --output1
/scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/1_adapter_removal/pair_1_adptr_rem.fastq
--output2
/scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/1_adapter_removal/pair_2_adptr_rem.fastq
--singleton
/scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/1_adapter_removal/singletons_adptr_rem.fastq
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billytaj
commented on August 23, 2024
Threads: What are the parallelism limits on this program? I am using an 80-thread core machine to run your program.
outputs: yes, pair_1_adptr_rem.fastq, pair_2_adptr_rem.fastq and singletons_adptr_rem.fastq are completely blank.
Are they blank for you too?
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MikkelSchubert
commented on August 23, 2024
There are no hard-coded limits, but most of those threads will probably end
doing little more than waiting for the next chunk of FASTQ reads to be read
and (subsequently) written.
Output looks fine for me, using the same options that you did, with the
output file only being slightly smaller than the input (due to the
aforementioned false positives).
I should have asked this earlier, but can you copy/paste or attach the
STDERR output from AdapterRemoval? Also, what version are you using? See
'AdapterRemoval --version'.
…On Tue, Dec 18, 2018 at 7:56 PM Billy Taj ***@***.***> wrote:
Threads: What are the parallelism limits on this program? I am using an
80-thread core machine to run your program.
outputs: yes, pair_1_adptr_rem.fastq, pair_2_adptr_rem.fastq and
singletons_adptr_rem.fastq are completely blank.
Are they blank for you too?
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billytaj
commented on August 23, 2024
version: version 2.1.7. Is there a newer one?
Oh, I see. it's a malformed header
Trimming paired end reads ... Error reading FASTQ record at line 1; aborting: Malformed or empty FASTQ header
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billytaj
commented on August 23, 2024
I don't really understand this error.
Does this program need "/1" and "/2" at the end of each fastq ID for paired-end mode?
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MikkelSchubert
commented on August 23, 2024
No, the /1 and /2 are not required. But if they are there, then they just
have to make sense (i.e. a 1 and a 2).
However, this particular error message is caused by the header line either
being empty or not starting with '@'.
Try to 'head' your input files and let me know what the result is?
…On Tue, Dec 18, 2018 at 8:30 PM Billy Taj ***@***.***> wrote:
I don't really understand this error.
Does this program need "/1" and "/2" at the end of each fastq ID for
paired-end mode?
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billytaj
commented on August 23, 2024
The fault is with my own code, and not an issue with yours. Thank you again for your help.
My particular issue is due to a Pandas import error making a mess of my input file.
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Related Issues (20)
- --combined-output generates strange GC% distribution in fastqc reports HOT 4
- stdout and stderr reversed? HOT 1
- homebrew/science was deprecated HOT 1
- Adapter Removal running error HOT 2
- Internal barcodes HOT 5
- Support JSON log output HOT 3
- Add option for singular 'combined' output FASTQ files HOT 5
- Input file is overwritten and cut off HOT 3
- Adapters Not Being Trimmed (Apparently)? HOT 2
- collapse with SE reads HOT 3
- How to demultiplexing paired-end reads in mixed orientation? HOT 4
- installation Adapterremoval with Conda HOT 2
- AdapterRemoval v3 Feedback HOT 12
- remove adapters sequences from BGI/MGI platform HOT 1
- combine with other QC tools HOT 1
- How to interpret the outputs of the multiple inputs after trimming? HOT 4
- New version of catch.hpp needed for glibc >= 2.34 HOT 1
- [feature request] Add support for GNU make's staged install via DESTDIR flag HOT 1
- support .gz format fastq as input HOT 1
- adapterremoval add windows version HOT 2
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